Variant report

Variant	rs6898415
Chromosome Location	chr5:126429749-126429750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10037625	0.89[EUR][1000 genomes]
rs10038644	0.82[EUR][1000 genomes]
rs10041457	0.82[EUR][1000 genomes]
rs10051184	0.86[EUR][1000 genomes]
rs10062622	0.84[EUR][1000 genomes]
rs1034844	0.83[GIH][hapmap]
rs108558	0.87[EUR][1000 genomes]
rs10900789	0.83[GIH][hapmap]
rs11241913	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs11241916	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12515192	0.85[GIH][hapmap]
rs12655220	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs12659065	0.80[AMR][1000 genomes]
rs13178353	0.86[EUR][1000 genomes]
rs13190493	0.82[EUR][1000 genomes]
rs1543815	0.83[EUR][1000 genomes]
rs1860440	0.81[EUR][1000 genomes]
rs2041318	0.80[EUR][1000 genomes]
rs2109215	0.96[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2191209	0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs2240527	0.83[GIH][hapmap]
rs2240528	0.83[GIH][hapmap]
rs2408788	0.83[EUR][1000 genomes]
rs2408789	0.83[EUR][1000 genomes]
rs2408790	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs248040	0.92[CEU][hapmap]
rs248062	0.90[EUR][1000 genomes]
rs248092	0.81[EUR][1000 genomes]
rs248095	0.80[EUR][1000 genomes]
rs248096	0.80[EUR][1000 genomes]
rs248102	0.80[EUR][1000 genomes]
rs248105	0.86[EUR][1000 genomes]
rs248107	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs248108	0.80[EUR][1000 genomes]
rs248109	0.87[EUR][1000 genomes]
rs248113	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs248118	0.87[EUR][1000 genomes]
rs248121	0.87[EUR][1000 genomes]
rs248126	0.85[EUR][1000 genomes]
rs2585204	0.85[EUR][1000 genomes]
rs3915634	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3936304	0.84[EUR][1000 genomes]
rs3936305	0.84[EUR][1000 genomes]
rs4380710	0.88[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs4836307	0.83[GIH][hapmap]
rs4836310	0.82[EUR][1000 genomes]
rs4836313	0.81[EUR][1000 genomes]
rs57555006	0.84[EUR][1000 genomes]
rs6595746	0.86[EUR][1000 genomes]
rs6859962	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6861348	0.86[EUR][1000 genomes]
rs6864668	0.89[EUR][1000 genomes]
rs6873502	0.82[EUR][1000 genomes]
rs6875043	0.84[EUR][1000 genomes]
rs6879393	0.89[EUR][1000 genomes]
rs6881948	0.82[EUR][1000 genomes]
rs6883106	0.83[EUR][1000 genomes]
rs6883627	0.82[EUR][1000 genomes]
rs6883672	0.94[EUR][1000 genomes]
rs6884988	0.81[EUR][1000 genomes]
rs6891436	0.82[GIH][hapmap]
rs726990	0.85[EUR][1000 genomes]
rs727038	0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs729607	0.83[GIH][hapmap]
rs7706333	0.85[GIH][hapmap]
rs7731621	0.82[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs7733551	0.83[GIH][hapmap]
rs7734890	0.81[EUR][1000 genomes]
rs7736693	0.85[GIH][hapmap]
rs990743	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv869897	chr5:126224358-126445210	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1816248	chr5:126399039-126486539	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6898415	C5orf63	cis	Nerve Tibial	GTEx
rs6898415	MARCH3	cis	Muscle Skeletal	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126424800-126429800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr5:126425400-126432200	Weak transcription	Fetal Thymus	thymus
3	chr5:126427200-126430200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:126427600-126430800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:126428000-126432400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:126428000-126434000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:126428400-126430800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:126428800-126430000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:126428800-126430000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:126428800-126430000	Weak transcription	Fetal Heart	heart
11	chr5:126428800-126430200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:126428800-126430200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:126428800-126430200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:126428800-126430200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:126428800-126430200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:126428800-126430400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:126428800-126431400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:126428800-126431400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:126428800-126432200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:126428800-126433200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:126429000-126430200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:126429000-126431000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:126429400-126430200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr5:126429400-126431000	Enhancers	Brain Anterior Caudate	brain
25	chr5:126429400-126431200	Enhancers	Fetal Intestine Large	intestine
26	chr5:126429600-126431200	Enhancers	Brain Substantia Nigra	brain
27	chr5:126429600-126431400	Enhancers	Fetal Intestine Small	intestine

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